Multiple sequence alignment - TraesCS5A01G061300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G061300 chr5A 100.000 3135 0 0 1 3135 64942524 64945658 0.000000e+00 5790.0
1 TraesCS5A01G061300 chr5A 91.667 348 18 1 1622 1958 64950416 64950763 3.660000e-129 472.0
2 TraesCS5A01G061300 chr5A 74.221 1187 232 46 600 1740 2929238 2930396 2.230000e-116 429.0
3 TraesCS5A01G061300 chr5A 73.986 1184 240 41 600 1740 3032954 3034112 4.840000e-113 418.0
4 TraesCS5A01G061300 chr5A 73.881 1206 237 45 578 1744 2934662 2935828 8.090000e-111 411.0
5 TraesCS5A01G061300 chr5B 92.204 1860 124 15 410 2259 82046054 82044206 0.000000e+00 2612.0
6 TraesCS5A01G061300 chr5B 97.211 1434 33 5 1703 3135 81617901 81616474 0.000000e+00 2420.0
7 TraesCS5A01G061300 chr5B 91.800 1317 87 12 410 1709 81625669 81624357 0.000000e+00 1814.0
8 TraesCS5A01G061300 chr5B 82.174 1150 154 19 1173 2294 81562407 81561281 0.000000e+00 941.0
9 TraesCS5A01G061300 chr5B 76.023 1197 208 50 578 1744 81782386 81781239 5.910000e-152 547.0
10 TraesCS5A01G061300 chr5B 83.094 556 83 6 612 1161 81571448 81570898 2.170000e-136 496.0
11 TraesCS5A01G061300 chr5B 74.120 568 120 20 1671 2228 82169503 82168953 3.170000e-50 209.0
12 TraesCS5A01G061300 chr5B 74.892 462 84 28 1911 2357 81781186 81780742 6.910000e-42 182.0
13 TraesCS5A01G061300 chr5B 96.386 83 3 0 228 310 81625805 81625723 1.520000e-28 137.0
14 TraesCS5A01G061300 chr5D 87.568 2027 193 26 354 2351 72491841 72493837 0.000000e+00 2292.0
15 TraesCS5A01G061300 chr5D 76.754 1226 245 22 537 1739 72362207 72363415 0.000000e+00 649.0
16 TraesCS5A01G061300 chr5D 76.485 1195 209 46 578 1744 72400920 72402070 4.510000e-163 584.0
17 TraesCS5A01G061300 chr5D 80.776 567 90 13 578 1133 6932923 6932365 2.890000e-115 425.0
18 TraesCS5A01G061300 chr5D 100.000 28 0 0 2374 2401 241954948 241954921 6.000000e-03 52.8
19 TraesCS5A01G061300 chr1D 81.553 103 18 1 575 676 485249245 485249347 2.000000e-12 84.2
20 TraesCS5A01G061300 chr3A 82.796 93 11 4 842 933 25038372 25038460 9.320000e-11 78.7
21 TraesCS5A01G061300 chr1A 80.769 104 17 3 575 676 582534830 582534932 9.320000e-11 78.7
22 TraesCS5A01G061300 chr2B 82.955 88 9 6 591 675 76073390 76073474 1.210000e-09 75.0
23 TraesCS5A01G061300 chr2A 97.297 37 1 0 2364 2400 771185654 771185690 2.610000e-06 63.9
24 TraesCS5A01G061300 chr3D 100.000 28 0 0 2374 2401 452490044 452490017 6.000000e-03 52.8
25 TraesCS5A01G061300 chr1B 100.000 28 0 0 2374 2401 276137631 276137658 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G061300 chr5A 64942524 64945658 3134 False 5790.0 5790 100.0000 1 3135 1 chr5A.!!$F4 3134
1 TraesCS5A01G061300 chr5A 2929238 2930396 1158 False 429.0 429 74.2210 600 1740 1 chr5A.!!$F1 1140
2 TraesCS5A01G061300 chr5A 3032954 3034112 1158 False 418.0 418 73.9860 600 1740 1 chr5A.!!$F3 1140
3 TraesCS5A01G061300 chr5A 2934662 2935828 1166 False 411.0 411 73.8810 578 1744 1 chr5A.!!$F2 1166
4 TraesCS5A01G061300 chr5B 82044206 82046054 1848 True 2612.0 2612 92.2040 410 2259 1 chr5B.!!$R4 1849
5 TraesCS5A01G061300 chr5B 81616474 81617901 1427 True 2420.0 2420 97.2110 1703 3135 1 chr5B.!!$R3 1432
6 TraesCS5A01G061300 chr5B 81624357 81625805 1448 True 975.5 1814 94.0930 228 1709 2 chr5B.!!$R6 1481
7 TraesCS5A01G061300 chr5B 81561281 81562407 1126 True 941.0 941 82.1740 1173 2294 1 chr5B.!!$R1 1121
8 TraesCS5A01G061300 chr5B 81570898 81571448 550 True 496.0 496 83.0940 612 1161 1 chr5B.!!$R2 549
9 TraesCS5A01G061300 chr5B 81780742 81782386 1644 True 364.5 547 75.4575 578 2357 2 chr5B.!!$R7 1779
10 TraesCS5A01G061300 chr5B 82168953 82169503 550 True 209.0 209 74.1200 1671 2228 1 chr5B.!!$R5 557
11 TraesCS5A01G061300 chr5D 72491841 72493837 1996 False 2292.0 2292 87.5680 354 2351 1 chr5D.!!$F3 1997
12 TraesCS5A01G061300 chr5D 72362207 72363415 1208 False 649.0 649 76.7540 537 1739 1 chr5D.!!$F1 1202
13 TraesCS5A01G061300 chr5D 72400920 72402070 1150 False 584.0 584 76.4850 578 1744 1 chr5D.!!$F2 1166
14 TraesCS5A01G061300 chr5D 6932365 6932923 558 True 425.0 425 80.7760 578 1133 1 chr5D.!!$R1 555

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
94 95 0.105593 CATAGCAGTGCACGGGAGAT 59.894 55.0 19.2 8.21 0.0 2.75 F
96 97 0.175760 TAGCAGTGCACGGGAGATTC 59.824 55.0 19.2 0.60 0.0 2.52 F
1147 1207 0.400213 ATCAAAGTCGGGTTGCTGGA 59.600 50.0 0.0 0.00 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1221 0.766131 TAGCACCCCCTTGTCGAAAA 59.234 50.000 0.0 0.0 0.0 2.29 R
1199 1259 0.958382 TCGCTTGTAACCCATGTGCC 60.958 55.000 0.0 0.0 0.0 5.01 R
2413 2557 1.302511 GCGCCTCCCTCTTGTTCAA 60.303 57.895 0.0 0.0 0.0 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.562408 TTTTACTTTGTATGTAGTCCATGTTGA 57.438 29.630 0.00 0.00 34.86 3.18
28 29 9.562408 TTTACTTTGTATGTAGTCCATGTTGAA 57.438 29.630 0.00 0.00 34.86 2.69
29 30 9.562408 TTACTTTGTATGTAGTCCATGTTGAAA 57.438 29.630 0.00 0.00 34.86 2.69
30 31 8.635765 ACTTTGTATGTAGTCCATGTTGAAAT 57.364 30.769 0.00 0.00 34.86 2.17
31 32 8.730680 ACTTTGTATGTAGTCCATGTTGAAATC 58.269 33.333 0.00 0.00 34.86 2.17
32 33 8.862325 TTTGTATGTAGTCCATGTTGAAATCT 57.138 30.769 0.00 0.00 34.86 2.40
33 34 8.492673 TTGTATGTAGTCCATGTTGAAATCTC 57.507 34.615 0.00 0.00 34.86 2.75
34 35 7.851228 TGTATGTAGTCCATGTTGAAATCTCT 58.149 34.615 0.00 0.00 34.86 3.10
35 36 7.765819 TGTATGTAGTCCATGTTGAAATCTCTG 59.234 37.037 0.00 0.00 34.86 3.35
36 37 6.358974 TGTAGTCCATGTTGAAATCTCTGA 57.641 37.500 0.00 0.00 0.00 3.27
37 38 6.768483 TGTAGTCCATGTTGAAATCTCTGAA 58.232 36.000 0.00 0.00 0.00 3.02
38 39 7.223584 TGTAGTCCATGTTGAAATCTCTGAAA 58.776 34.615 0.00 0.00 0.00 2.69
39 40 7.719193 TGTAGTCCATGTTGAAATCTCTGAAAA 59.281 33.333 0.00 0.00 0.00 2.29
40 41 7.211966 AGTCCATGTTGAAATCTCTGAAAAG 57.788 36.000 0.00 0.00 0.00 2.27
41 42 7.000472 AGTCCATGTTGAAATCTCTGAAAAGA 59.000 34.615 0.00 0.00 0.00 2.52
42 43 7.040823 AGTCCATGTTGAAATCTCTGAAAAGAC 60.041 37.037 0.00 0.00 0.00 3.01
43 44 7.000472 TCCATGTTGAAATCTCTGAAAAGACT 59.000 34.615 0.00 0.00 0.00 3.24
44 45 7.503566 TCCATGTTGAAATCTCTGAAAAGACTT 59.496 33.333 0.00 0.00 0.00 3.01
45 46 8.786898 CCATGTTGAAATCTCTGAAAAGACTTA 58.213 33.333 0.00 0.00 0.00 2.24
46 47 9.823098 CATGTTGAAATCTCTGAAAAGACTTAG 57.177 33.333 0.00 0.00 0.00 2.18
47 48 8.383318 TGTTGAAATCTCTGAAAAGACTTAGG 57.617 34.615 0.00 0.00 0.00 2.69
48 49 8.210946 TGTTGAAATCTCTGAAAAGACTTAGGA 58.789 33.333 0.00 0.00 0.00 2.94
49 50 9.057089 GTTGAAATCTCTGAAAAGACTTAGGAA 57.943 33.333 0.00 0.00 0.00 3.36
50 51 8.608844 TGAAATCTCTGAAAAGACTTAGGAAC 57.391 34.615 0.00 0.00 0.00 3.62
51 52 8.210946 TGAAATCTCTGAAAAGACTTAGGAACA 58.789 33.333 0.00 0.00 0.00 3.18
52 53 8.614469 AAATCTCTGAAAAGACTTAGGAACAG 57.386 34.615 0.00 0.00 0.00 3.16
53 54 6.102897 TCTCTGAAAAGACTTAGGAACAGG 57.897 41.667 0.00 0.00 0.00 4.00
54 55 5.012148 TCTCTGAAAAGACTTAGGAACAGGG 59.988 44.000 0.00 0.00 0.00 4.45
55 56 4.905456 TCTGAAAAGACTTAGGAACAGGGA 59.095 41.667 0.00 0.00 0.00 4.20
56 57 5.012148 TCTGAAAAGACTTAGGAACAGGGAG 59.988 44.000 0.00 0.00 0.00 4.30
57 58 4.658901 TGAAAAGACTTAGGAACAGGGAGT 59.341 41.667 0.00 0.00 0.00 3.85
58 59 5.842328 TGAAAAGACTTAGGAACAGGGAGTA 59.158 40.000 0.00 0.00 0.00 2.59
59 60 5.741962 AAAGACTTAGGAACAGGGAGTAC 57.258 43.478 0.00 0.00 0.00 2.73
60 61 4.678538 AGACTTAGGAACAGGGAGTACT 57.321 45.455 0.00 0.00 0.00 2.73
61 62 5.013258 AGACTTAGGAACAGGGAGTACTT 57.987 43.478 0.00 0.00 0.00 2.24
62 63 6.150034 AGACTTAGGAACAGGGAGTACTTA 57.850 41.667 0.00 0.00 0.00 2.24
63 64 6.189133 AGACTTAGGAACAGGGAGTACTTAG 58.811 44.000 0.00 0.00 0.00 2.18
64 65 4.710865 ACTTAGGAACAGGGAGTACTTAGC 59.289 45.833 0.00 0.00 0.00 3.09
65 66 2.100989 AGGAACAGGGAGTACTTAGCG 58.899 52.381 0.00 0.00 0.00 4.26
66 67 2.097825 GGAACAGGGAGTACTTAGCGA 58.902 52.381 0.00 0.00 0.00 4.93
67 68 2.494870 GGAACAGGGAGTACTTAGCGAA 59.505 50.000 0.00 0.00 0.00 4.70
68 69 3.056322 GGAACAGGGAGTACTTAGCGAAA 60.056 47.826 0.00 0.00 0.00 3.46
69 70 4.382793 GGAACAGGGAGTACTTAGCGAAAT 60.383 45.833 0.00 0.00 0.00 2.17
70 71 4.820894 ACAGGGAGTACTTAGCGAAATT 57.179 40.909 0.00 0.00 0.00 1.82
71 72 5.927281 ACAGGGAGTACTTAGCGAAATTA 57.073 39.130 0.00 0.00 0.00 1.40
72 73 6.481434 ACAGGGAGTACTTAGCGAAATTAT 57.519 37.500 0.00 0.00 0.00 1.28
73 74 6.885922 ACAGGGAGTACTTAGCGAAATTATT 58.114 36.000 0.00 0.00 0.00 1.40
74 75 7.336396 ACAGGGAGTACTTAGCGAAATTATTT 58.664 34.615 0.00 0.00 0.00 1.40
75 76 7.494952 ACAGGGAGTACTTAGCGAAATTATTTC 59.505 37.037 7.56 7.56 36.32 2.17
76 77 7.494625 CAGGGAGTACTTAGCGAAATTATTTCA 59.505 37.037 16.57 0.00 39.63 2.69
77 78 8.211629 AGGGAGTACTTAGCGAAATTATTTCAT 58.788 33.333 16.57 7.79 39.63 2.57
78 79 9.485206 GGGAGTACTTAGCGAAATTATTTCATA 57.515 33.333 16.57 6.93 39.63 2.15
81 82 9.542462 AGTACTTAGCGAAATTATTTCATAGCA 57.458 29.630 16.57 2.66 39.63 3.49
82 83 9.798885 GTACTTAGCGAAATTATTTCATAGCAG 57.201 33.333 16.57 9.15 39.63 4.24
83 84 8.438676 ACTTAGCGAAATTATTTCATAGCAGT 57.561 30.769 16.57 9.64 39.63 4.40
84 85 8.338259 ACTTAGCGAAATTATTTCATAGCAGTG 58.662 33.333 16.57 8.61 39.63 3.66
85 86 5.514279 AGCGAAATTATTTCATAGCAGTGC 58.486 37.500 16.57 7.13 39.63 4.40
86 87 5.066375 AGCGAAATTATTTCATAGCAGTGCA 59.934 36.000 19.20 3.62 39.63 4.57
87 88 5.172053 GCGAAATTATTTCATAGCAGTGCAC 59.828 40.000 19.20 9.40 39.63 4.57
88 89 5.393452 CGAAATTATTTCATAGCAGTGCACG 59.607 40.000 19.20 7.77 39.63 5.34
89 90 4.818534 ATTATTTCATAGCAGTGCACGG 57.181 40.909 19.20 13.06 0.00 4.94
90 91 1.382522 ATTTCATAGCAGTGCACGGG 58.617 50.000 19.20 12.74 0.00 5.28
91 92 0.323302 TTTCATAGCAGTGCACGGGA 59.677 50.000 19.20 6.29 0.00 5.14
92 93 0.108186 TTCATAGCAGTGCACGGGAG 60.108 55.000 19.20 8.06 0.00 4.30
93 94 0.970427 TCATAGCAGTGCACGGGAGA 60.970 55.000 19.20 7.31 0.00 3.71
94 95 0.105593 CATAGCAGTGCACGGGAGAT 59.894 55.000 19.20 8.21 0.00 2.75
95 96 0.833287 ATAGCAGTGCACGGGAGATT 59.167 50.000 19.20 0.00 0.00 2.40
96 97 0.175760 TAGCAGTGCACGGGAGATTC 59.824 55.000 19.20 0.60 0.00 2.52
97 98 2.109126 GCAGTGCACGGGAGATTCC 61.109 63.158 18.78 0.00 35.23 3.01
98 99 1.296392 CAGTGCACGGGAGATTCCA 59.704 57.895 12.01 0.00 38.64 3.53
99 100 0.742281 CAGTGCACGGGAGATTCCAG 60.742 60.000 12.01 0.00 38.64 3.86
100 101 2.109126 GTGCACGGGAGATTCCAGC 61.109 63.158 0.00 0.00 38.64 4.85
101 102 2.514824 GCACGGGAGATTCCAGCC 60.515 66.667 0.00 0.00 38.64 4.85
102 103 2.190578 CACGGGAGATTCCAGCCC 59.809 66.667 0.00 0.00 38.64 5.19
103 104 2.285368 ACGGGAGATTCCAGCCCA 60.285 61.111 0.00 0.00 42.14 5.36
104 105 2.370445 ACGGGAGATTCCAGCCCAG 61.370 63.158 0.00 0.00 42.14 4.45
105 106 2.194326 GGGAGATTCCAGCCCAGC 59.806 66.667 0.00 0.00 41.64 4.85
106 107 2.381941 GGGAGATTCCAGCCCAGCT 61.382 63.158 0.00 0.00 41.64 4.24
107 108 1.148048 GGAGATTCCAGCCCAGCTC 59.852 63.158 0.00 0.00 36.40 4.09
108 109 1.227497 GAGATTCCAGCCCAGCTCG 60.227 63.158 0.00 0.00 36.40 5.03
109 110 2.203126 GATTCCAGCCCAGCTCGG 60.203 66.667 0.00 0.00 36.40 4.63
128 129 4.748144 CCAGCCCAGCCCAAGGAC 62.748 72.222 0.00 0.00 0.00 3.85
129 130 3.970410 CAGCCCAGCCCAAGGACA 61.970 66.667 0.00 0.00 0.00 4.02
130 131 3.971702 AGCCCAGCCCAAGGACAC 61.972 66.667 0.00 0.00 0.00 3.67
131 132 4.284550 GCCCAGCCCAAGGACACA 62.285 66.667 0.00 0.00 0.00 3.72
132 133 2.765969 CCCAGCCCAAGGACACAT 59.234 61.111 0.00 0.00 0.00 3.21
133 134 1.998530 CCCAGCCCAAGGACACATA 59.001 57.895 0.00 0.00 0.00 2.29
134 135 0.552848 CCCAGCCCAAGGACACATAT 59.447 55.000 0.00 0.00 0.00 1.78
135 136 1.063717 CCCAGCCCAAGGACACATATT 60.064 52.381 0.00 0.00 0.00 1.28
136 137 2.301346 CCAGCCCAAGGACACATATTC 58.699 52.381 0.00 0.00 0.00 1.75
137 138 2.357050 CCAGCCCAAGGACACATATTCA 60.357 50.000 0.00 0.00 0.00 2.57
138 139 3.559069 CAGCCCAAGGACACATATTCAT 58.441 45.455 0.00 0.00 0.00 2.57
139 140 3.956199 CAGCCCAAGGACACATATTCATT 59.044 43.478 0.00 0.00 0.00 2.57
140 141 4.037208 CAGCCCAAGGACACATATTCATTC 59.963 45.833 0.00 0.00 0.00 2.67
141 142 3.003689 GCCCAAGGACACATATTCATTCG 59.996 47.826 0.00 0.00 0.00 3.34
142 143 4.199310 CCCAAGGACACATATTCATTCGT 58.801 43.478 0.00 0.00 0.00 3.85
143 144 4.273480 CCCAAGGACACATATTCATTCGTC 59.727 45.833 0.00 0.00 0.00 4.20
144 145 4.875536 CCAAGGACACATATTCATTCGTCA 59.124 41.667 0.00 0.00 0.00 4.35
145 146 5.220662 CCAAGGACACATATTCATTCGTCAC 60.221 44.000 0.00 0.00 0.00 3.67
146 147 5.344743 AGGACACATATTCATTCGTCACT 57.655 39.130 0.00 0.00 0.00 3.41
147 148 6.465439 AGGACACATATTCATTCGTCACTA 57.535 37.500 0.00 0.00 0.00 2.74
148 149 6.873997 AGGACACATATTCATTCGTCACTAA 58.126 36.000 0.00 0.00 0.00 2.24
149 150 6.980978 AGGACACATATTCATTCGTCACTAAG 59.019 38.462 0.00 0.00 0.00 2.18
150 151 6.978659 GGACACATATTCATTCGTCACTAAGA 59.021 38.462 0.00 0.00 0.00 2.10
151 152 7.491372 GGACACATATTCATTCGTCACTAAGAA 59.509 37.037 0.00 0.00 0.00 2.52
152 153 8.771920 ACACATATTCATTCGTCACTAAGAAA 57.228 30.769 0.00 0.00 0.00 2.52
153 154 9.214957 ACACATATTCATTCGTCACTAAGAAAA 57.785 29.630 0.00 0.00 0.00 2.29
156 157 9.708222 CATATTCATTCGTCACTAAGAAAAAGG 57.292 33.333 0.00 0.00 0.00 3.11
157 158 6.554334 TTCATTCGTCACTAAGAAAAAGGG 57.446 37.500 0.00 0.00 0.00 3.95
158 159 5.001232 TCATTCGTCACTAAGAAAAAGGGG 58.999 41.667 0.00 0.00 0.00 4.79
159 160 4.693042 TTCGTCACTAAGAAAAAGGGGA 57.307 40.909 0.00 0.00 0.00 4.81
160 161 4.267349 TCGTCACTAAGAAAAAGGGGAG 57.733 45.455 0.00 0.00 0.00 4.30
161 162 3.644738 TCGTCACTAAGAAAAAGGGGAGT 59.355 43.478 0.00 0.00 0.00 3.85
162 163 4.834496 TCGTCACTAAGAAAAAGGGGAGTA 59.166 41.667 0.00 0.00 0.00 2.59
163 164 4.928020 CGTCACTAAGAAAAAGGGGAGTAC 59.072 45.833 0.00 0.00 0.00 2.73
164 165 5.510179 CGTCACTAAGAAAAAGGGGAGTACA 60.510 44.000 0.00 0.00 0.00 2.90
165 166 6.293698 GTCACTAAGAAAAAGGGGAGTACAA 58.706 40.000 0.00 0.00 0.00 2.41
166 167 6.769341 GTCACTAAGAAAAAGGGGAGTACAAA 59.231 38.462 0.00 0.00 0.00 2.83
167 168 7.447545 GTCACTAAGAAAAAGGGGAGTACAAAT 59.552 37.037 0.00 0.00 0.00 2.32
168 169 8.002459 TCACTAAGAAAAAGGGGAGTACAAATT 58.998 33.333 0.00 0.00 0.00 1.82
169 170 8.297426 CACTAAGAAAAAGGGGAGTACAAATTC 58.703 37.037 0.00 0.00 0.00 2.17
170 171 5.959618 AGAAAAAGGGGAGTACAAATTCG 57.040 39.130 0.00 0.00 0.00 3.34
171 172 4.765339 AGAAAAAGGGGAGTACAAATTCGG 59.235 41.667 0.00 0.00 0.00 4.30
172 173 3.801307 AAAGGGGAGTACAAATTCGGT 57.199 42.857 0.00 0.00 0.00 4.69
173 174 3.345508 AAGGGGAGTACAAATTCGGTC 57.654 47.619 0.00 0.00 0.00 4.79
174 175 1.206371 AGGGGAGTACAAATTCGGTCG 59.794 52.381 0.00 0.00 0.00 4.79
175 176 1.066645 GGGGAGTACAAATTCGGTCGT 60.067 52.381 0.00 0.00 0.00 4.34
176 177 2.613725 GGGGAGTACAAATTCGGTCGTT 60.614 50.000 0.00 0.00 0.00 3.85
177 178 2.669924 GGGAGTACAAATTCGGTCGTTC 59.330 50.000 0.00 0.00 0.00 3.95
178 179 3.582780 GGAGTACAAATTCGGTCGTTCT 58.417 45.455 0.00 0.00 0.00 3.01
179 180 3.992427 GGAGTACAAATTCGGTCGTTCTT 59.008 43.478 0.00 0.00 0.00 2.52
180 181 4.091075 GGAGTACAAATTCGGTCGTTCTTC 59.909 45.833 0.00 0.00 0.00 2.87
181 182 4.624015 AGTACAAATTCGGTCGTTCTTCA 58.376 39.130 0.00 0.00 0.00 3.02
182 183 5.235516 AGTACAAATTCGGTCGTTCTTCAT 58.764 37.500 0.00 0.00 0.00 2.57
183 184 5.699458 AGTACAAATTCGGTCGTTCTTCATT 59.301 36.000 0.00 0.00 0.00 2.57
184 185 5.432885 ACAAATTCGGTCGTTCTTCATTT 57.567 34.783 0.00 0.00 0.00 2.32
185 186 5.449304 ACAAATTCGGTCGTTCTTCATTTC 58.551 37.500 0.00 0.00 0.00 2.17
186 187 5.238650 ACAAATTCGGTCGTTCTTCATTTCT 59.761 36.000 0.00 0.00 0.00 2.52
187 188 4.928661 ATTCGGTCGTTCTTCATTTCTG 57.071 40.909 0.00 0.00 0.00 3.02
188 189 3.653539 TCGGTCGTTCTTCATTTCTGA 57.346 42.857 0.00 0.00 0.00 3.27
189 190 3.985008 TCGGTCGTTCTTCATTTCTGAA 58.015 40.909 0.00 0.00 39.07 3.02
197 198 0.881118 TTCATTTCTGAAGCCACCGC 59.119 50.000 0.00 0.00 36.46 5.68
212 213 4.107051 CGCTGCCGCCTCCTTTTG 62.107 66.667 0.00 0.00 0.00 2.44
213 214 4.426112 GCTGCCGCCTCCTTTTGC 62.426 66.667 0.00 0.00 0.00 3.68
214 215 3.752339 CTGCCGCCTCCTTTTGCC 61.752 66.667 0.00 0.00 0.00 4.52
215 216 4.284550 TGCCGCCTCCTTTTGCCT 62.285 61.111 0.00 0.00 0.00 4.75
216 217 2.991540 GCCGCCTCCTTTTGCCTT 60.992 61.111 0.00 0.00 0.00 4.35
217 218 2.964978 CCGCCTCCTTTTGCCTTG 59.035 61.111 0.00 0.00 0.00 3.61
218 219 2.639327 CCGCCTCCTTTTGCCTTGG 61.639 63.158 0.00 0.00 0.00 3.61
219 220 2.659016 GCCTCCTTTTGCCTTGGC 59.341 61.111 4.43 4.43 0.00 4.52
220 221 2.947532 GCCTCCTTTTGCCTTGGCC 61.948 63.158 9.35 0.00 34.81 5.36
221 222 2.285773 CCTCCTTTTGCCTTGGCCC 61.286 63.158 9.35 0.00 0.00 5.80
222 223 2.600173 TCCTTTTGCCTTGGCCCG 60.600 61.111 9.35 0.00 0.00 6.13
223 224 4.377708 CCTTTTGCCTTGGCCCGC 62.378 66.667 9.35 0.00 0.00 6.13
224 225 4.377708 CTTTTGCCTTGGCCCGCC 62.378 66.667 9.35 0.00 0.00 6.13
272 273 2.046892 CACTGCTTCCACTCCCCG 60.047 66.667 0.00 0.00 0.00 5.73
303 304 2.580601 CGTCCTCCGAACCCCAGTT 61.581 63.158 0.00 0.00 39.56 3.16
337 354 3.869272 CATCTCCGGCGCTGTTGC 61.869 66.667 16.49 0.00 0.00 4.17
344 361 2.202479 GGCGCTGTTGCCGATTTC 60.202 61.111 7.64 0.00 46.75 2.17
345 362 2.202479 GCGCTGTTGCCGATTTCC 60.202 61.111 0.00 0.00 35.36 3.13
346 363 2.485122 CGCTGTTGCCGATTTCCC 59.515 61.111 0.00 0.00 35.36 3.97
347 364 2.885113 GCTGTTGCCGATTTCCCC 59.115 61.111 0.00 0.00 0.00 4.81
348 365 2.710902 GCTGTTGCCGATTTCCCCC 61.711 63.158 0.00 0.00 0.00 5.40
349 366 2.360600 TGTTGCCGATTTCCCCCG 60.361 61.111 0.00 0.00 0.00 5.73
351 368 3.653078 TTGCCGATTTCCCCCGGT 61.653 61.111 0.00 0.00 46.84 5.28
352 369 2.299429 TTGCCGATTTCCCCCGGTA 61.299 57.895 0.00 0.00 46.84 4.02
360 377 0.688487 TTTCCCCCGGTACACTTCAG 59.312 55.000 0.00 0.00 0.00 3.02
373 390 1.338020 CACTTCAGCTGAAAACCACCC 59.662 52.381 28.16 0.00 33.07 4.61
375 392 2.242043 CTTCAGCTGAAAACCACCCAT 58.758 47.619 28.16 0.00 33.07 4.00
376 393 3.181434 ACTTCAGCTGAAAACCACCCATA 60.181 43.478 28.16 3.43 33.07 2.74
390 407 4.410883 ACCACCCATATTTCGATCCAGTAA 59.589 41.667 0.00 0.00 0.00 2.24
391 408 4.755123 CCACCCATATTTCGATCCAGTAAC 59.245 45.833 0.00 0.00 0.00 2.50
392 409 4.755123 CACCCATATTTCGATCCAGTAACC 59.245 45.833 0.00 0.00 0.00 2.85
393 410 3.994392 CCCATATTTCGATCCAGTAACCG 59.006 47.826 0.00 0.00 0.00 4.44
394 411 4.502604 CCCATATTTCGATCCAGTAACCGT 60.503 45.833 0.00 0.00 0.00 4.83
395 412 5.279106 CCCATATTTCGATCCAGTAACCGTA 60.279 44.000 0.00 0.00 0.00 4.02
427 444 2.433146 GCCTCCCTAGGGTTCCGAC 61.433 68.421 27.58 8.76 43.87 4.79
571 589 2.279120 GAGGATGTGCTCGCCGAG 60.279 66.667 10.36 10.36 0.00 4.63
1104 1164 2.658285 GAATCTGAATGGCCACCATCA 58.342 47.619 8.16 12.72 44.40 3.07
1109 1169 2.498481 CTGAATGGCCACCATCACAATT 59.502 45.455 8.16 0.00 44.40 2.32
1110 1170 3.700539 CTGAATGGCCACCATCACAATTA 59.299 43.478 8.16 0.00 44.40 1.40
1116 1176 5.514169 TGGCCACCATCACAATTAAAGATA 58.486 37.500 0.00 0.00 0.00 1.98
1147 1207 0.400213 ATCAAAGTCGGGTTGCTGGA 59.600 50.000 0.00 0.00 0.00 3.86
1161 1221 4.767409 GGTTGCTGGAAGGAGAAGTATTTT 59.233 41.667 0.00 0.00 33.89 1.82
1199 1259 3.430098 GCTACAGGGATTGTCAGTGAGAG 60.430 52.174 0.00 0.00 41.29 3.20
1251 1317 5.852229 CGTCTATTATCGAGGAGCACTTTAC 59.148 44.000 0.00 0.00 0.00 2.01
1256 1322 2.430465 TCGAGGAGCACTTTACGTACT 58.570 47.619 0.00 0.00 0.00 2.73
1263 1329 2.296471 AGCACTTTACGTACTCTGCAGT 59.704 45.455 14.67 0.00 36.55 4.40
1265 1331 3.639538 CACTTTACGTACTCTGCAGTGT 58.360 45.455 23.57 23.57 33.62 3.55
1267 1333 4.506654 CACTTTACGTACTCTGCAGTGTTT 59.493 41.667 25.01 13.10 33.62 2.83
1443 1529 2.534298 CAGAGCACACGACTATCCTTG 58.466 52.381 0.00 0.00 0.00 3.61
1525 1614 0.179029 AGCGTAAGTGTTGGCTTGGT 60.179 50.000 0.00 0.00 41.68 3.67
1560 1649 3.286329 TGAATCATGTGGTCAGATGGG 57.714 47.619 8.00 0.00 33.39 4.00
1630 1728 3.132289 ACCGATATTGTGGACGACTTCAT 59.868 43.478 0.00 0.00 0.00 2.57
1792 1896 4.275936 TGCTTAGAAGACAACAAGAAAGCC 59.724 41.667 0.00 0.00 37.80 4.35
1875 1979 1.543429 GGTTGAAGAGTGTCACTGGGG 60.543 57.143 11.04 0.00 0.00 4.96
1905 2027 9.343539 AGAGCATTATGATGATTCATATGATGG 57.656 33.333 6.17 0.00 42.86 3.51
1964 2086 7.822658 AGAGATTGTCTTCTTGAGTAGTACAC 58.177 38.462 2.52 0.00 27.07 2.90
2120 2242 5.016173 CCCCATGTTGGATTGAAGAGTTAA 58.984 41.667 0.00 0.00 40.96 2.01
2123 2245 6.884295 CCCATGTTGGATTGAAGAGTTAACTA 59.116 38.462 8.42 0.00 40.96 2.24
2370 2514 3.409804 ACTCCCTCCGTCCCTAAATAA 57.590 47.619 0.00 0.00 0.00 1.40
2447 2591 2.427095 AGGCGCCATTTATTCCAACTTC 59.573 45.455 31.54 0.00 0.00 3.01
2449 2593 3.367910 GGCGCCATTTATTCCAACTTCAA 60.368 43.478 24.80 0.00 0.00 2.69
2552 2696 9.846248 CTAGGAATGTGTATTTTTCCTTTTGAG 57.154 33.333 8.59 0.00 45.41 3.02
2586 2730 5.858381 TGTTAGCTTCAAACATCTCACTCT 58.142 37.500 0.00 0.00 32.07 3.24
2589 2733 5.686159 AGCTTCAAACATCTCACTCTTTG 57.314 39.130 0.00 0.00 0.00 2.77
2590 2734 4.518211 AGCTTCAAACATCTCACTCTTTGG 59.482 41.667 0.00 0.00 0.00 3.28
2591 2735 4.516698 GCTTCAAACATCTCACTCTTTGGA 59.483 41.667 0.00 0.00 0.00 3.53
2593 2737 6.564709 TTCAAACATCTCACTCTTTGGATG 57.435 37.500 0.00 0.00 38.18 3.51
2594 2738 5.868454 TCAAACATCTCACTCTTTGGATGA 58.132 37.500 8.48 0.00 36.83 2.92
2750 2894 7.417911 CCAGTAGCTACATGGATTCTAAGTCAA 60.418 40.741 25.95 0.00 36.09 3.18
2785 2929 5.337554 CGTCCTCTGTATGTATTGTTCGAA 58.662 41.667 0.00 0.00 0.00 3.71
2871 3015 0.788995 CTCAGCTGCACTTCGACAAG 59.211 55.000 9.47 0.00 35.50 3.16
2928 3072 1.688735 TCCAGTGTCTTGTCCTGACTG 59.311 52.381 0.00 0.00 35.63 3.51
2988 3132 1.001641 CTTGGTCCTTCCTGGCCTG 60.002 63.158 3.32 2.54 37.07 4.85
3015 3159 8.092068 TCATATACTGAACTTCGTTCCTTTCAA 58.908 33.333 4.48 0.00 41.35 2.69
3049 3193 5.808030 CACAATGAATATGCACAATGCTTCA 59.192 36.000 2.02 4.62 45.31 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.562408 TCAACATGGACTACATACAAAGTAAAA 57.438 29.630 0.00 0.00 37.84 1.52
2 3 9.562408 TTCAACATGGACTACATACAAAGTAAA 57.438 29.630 0.00 0.00 37.84 2.01
3 4 9.562408 TTTCAACATGGACTACATACAAAGTAA 57.438 29.630 0.00 0.00 37.84 2.24
4 5 9.733556 ATTTCAACATGGACTACATACAAAGTA 57.266 29.630 0.00 0.00 37.84 2.24
5 6 8.635765 ATTTCAACATGGACTACATACAAAGT 57.364 30.769 0.00 0.00 37.84 2.66
6 7 8.950210 AGATTTCAACATGGACTACATACAAAG 58.050 33.333 0.00 0.00 37.84 2.77
7 8 8.862325 AGATTTCAACATGGACTACATACAAA 57.138 30.769 0.00 0.00 37.84 2.83
8 9 8.321353 AGAGATTTCAACATGGACTACATACAA 58.679 33.333 0.00 0.00 37.84 2.41
9 10 7.765819 CAGAGATTTCAACATGGACTACATACA 59.234 37.037 0.00 0.00 37.84 2.29
10 11 7.981789 TCAGAGATTTCAACATGGACTACATAC 59.018 37.037 0.00 0.00 37.84 2.39
11 12 8.078060 TCAGAGATTTCAACATGGACTACATA 57.922 34.615 0.00 0.00 37.84 2.29
12 13 6.950842 TCAGAGATTTCAACATGGACTACAT 58.049 36.000 0.00 0.00 41.57 2.29
13 14 6.358974 TCAGAGATTTCAACATGGACTACA 57.641 37.500 0.00 0.00 0.00 2.74
14 15 7.672983 TTTCAGAGATTTCAACATGGACTAC 57.327 36.000 0.00 0.00 0.00 2.73
15 16 8.156820 TCTTTTCAGAGATTTCAACATGGACTA 58.843 33.333 0.00 0.00 0.00 2.59
16 17 7.000472 TCTTTTCAGAGATTTCAACATGGACT 59.000 34.615 0.00 0.00 0.00 3.85
17 18 7.040823 AGTCTTTTCAGAGATTTCAACATGGAC 60.041 37.037 0.00 0.00 0.00 4.02
18 19 7.000472 AGTCTTTTCAGAGATTTCAACATGGA 59.000 34.615 0.00 0.00 0.00 3.41
19 20 7.211966 AGTCTTTTCAGAGATTTCAACATGG 57.788 36.000 0.00 0.00 0.00 3.66
20 21 9.823098 CTAAGTCTTTTCAGAGATTTCAACATG 57.177 33.333 0.00 0.00 29.76 3.21
21 22 9.007901 CCTAAGTCTTTTCAGAGATTTCAACAT 57.992 33.333 0.00 0.00 29.76 2.71
22 23 8.210946 TCCTAAGTCTTTTCAGAGATTTCAACA 58.789 33.333 0.00 0.00 29.76 3.33
23 24 8.608844 TCCTAAGTCTTTTCAGAGATTTCAAC 57.391 34.615 0.00 0.00 29.76 3.18
24 25 9.057089 GTTCCTAAGTCTTTTCAGAGATTTCAA 57.943 33.333 0.00 0.00 29.76 2.69
25 26 8.210946 TGTTCCTAAGTCTTTTCAGAGATTTCA 58.789 33.333 0.00 0.00 29.76 2.69
26 27 8.608844 TGTTCCTAAGTCTTTTCAGAGATTTC 57.391 34.615 0.00 0.00 29.76 2.17
27 28 7.663493 CCTGTTCCTAAGTCTTTTCAGAGATTT 59.337 37.037 0.00 0.00 31.59 2.17
28 29 7.164803 CCTGTTCCTAAGTCTTTTCAGAGATT 58.835 38.462 0.00 0.00 0.00 2.40
29 30 6.296145 CCCTGTTCCTAAGTCTTTTCAGAGAT 60.296 42.308 0.00 0.00 0.00 2.75
30 31 5.012148 CCCTGTTCCTAAGTCTTTTCAGAGA 59.988 44.000 0.00 0.00 0.00 3.10
31 32 5.012148 TCCCTGTTCCTAAGTCTTTTCAGAG 59.988 44.000 0.00 0.00 0.00 3.35
32 33 4.905456 TCCCTGTTCCTAAGTCTTTTCAGA 59.095 41.667 0.00 0.00 0.00 3.27
33 34 5.221742 ACTCCCTGTTCCTAAGTCTTTTCAG 60.222 44.000 0.00 0.00 0.00 3.02
34 35 4.658901 ACTCCCTGTTCCTAAGTCTTTTCA 59.341 41.667 0.00 0.00 0.00 2.69
35 36 5.230323 ACTCCCTGTTCCTAAGTCTTTTC 57.770 43.478 0.00 0.00 0.00 2.29
36 37 5.845065 AGTACTCCCTGTTCCTAAGTCTTTT 59.155 40.000 0.00 0.00 0.00 2.27
37 38 5.404395 AGTACTCCCTGTTCCTAAGTCTTT 58.596 41.667 0.00 0.00 0.00 2.52
38 39 5.013258 AGTACTCCCTGTTCCTAAGTCTT 57.987 43.478 0.00 0.00 0.00 3.01
39 40 4.678538 AGTACTCCCTGTTCCTAAGTCT 57.321 45.455 0.00 0.00 0.00 3.24
40 41 5.163530 GCTAAGTACTCCCTGTTCCTAAGTC 60.164 48.000 0.00 0.00 0.00 3.01
41 42 4.710865 GCTAAGTACTCCCTGTTCCTAAGT 59.289 45.833 0.00 0.00 0.00 2.24
42 43 4.202030 CGCTAAGTACTCCCTGTTCCTAAG 60.202 50.000 0.00 0.00 0.00 2.18
43 44 3.698040 CGCTAAGTACTCCCTGTTCCTAA 59.302 47.826 0.00 0.00 0.00 2.69
44 45 3.054139 TCGCTAAGTACTCCCTGTTCCTA 60.054 47.826 0.00 0.00 0.00 2.94
45 46 2.100989 CGCTAAGTACTCCCTGTTCCT 58.899 52.381 0.00 0.00 0.00 3.36
46 47 2.097825 TCGCTAAGTACTCCCTGTTCC 58.902 52.381 0.00 0.00 0.00 3.62
47 48 3.863142 TTCGCTAAGTACTCCCTGTTC 57.137 47.619 0.00 0.00 0.00 3.18
48 49 4.820894 ATTTCGCTAAGTACTCCCTGTT 57.179 40.909 0.00 0.00 0.00 3.16
49 50 4.820894 AATTTCGCTAAGTACTCCCTGT 57.179 40.909 0.00 0.00 0.00 4.00
50 51 7.494625 TGAAATAATTTCGCTAAGTACTCCCTG 59.505 37.037 0.00 0.00 42.55 4.45
51 52 7.562135 TGAAATAATTTCGCTAAGTACTCCCT 58.438 34.615 0.00 0.00 42.55 4.20
52 53 7.781548 TGAAATAATTTCGCTAAGTACTCCC 57.218 36.000 0.00 0.00 42.55 4.30
55 56 9.542462 TGCTATGAAATAATTTCGCTAAGTACT 57.458 29.630 0.00 0.00 42.55 2.73
56 57 9.798885 CTGCTATGAAATAATTTCGCTAAGTAC 57.201 33.333 0.00 0.00 42.55 2.73
57 58 9.542462 ACTGCTATGAAATAATTTCGCTAAGTA 57.458 29.630 0.00 0.00 42.55 2.24
58 59 8.338259 CACTGCTATGAAATAATTTCGCTAAGT 58.662 33.333 0.00 0.00 42.55 2.24
59 60 7.322222 GCACTGCTATGAAATAATTTCGCTAAG 59.678 37.037 0.00 0.00 42.55 2.18
60 61 7.132213 GCACTGCTATGAAATAATTTCGCTAA 58.868 34.615 0.00 0.00 42.55 3.09
61 62 6.259829 TGCACTGCTATGAAATAATTTCGCTA 59.740 34.615 1.98 0.00 42.55 4.26
62 63 5.066375 TGCACTGCTATGAAATAATTTCGCT 59.934 36.000 1.98 0.00 42.55 4.93
63 64 5.172053 GTGCACTGCTATGAAATAATTTCGC 59.828 40.000 10.32 0.00 42.55 4.70
64 65 5.393452 CGTGCACTGCTATGAAATAATTTCG 59.607 40.000 16.19 0.00 42.55 3.46
65 66 5.682862 CCGTGCACTGCTATGAAATAATTTC 59.317 40.000 16.19 0.00 40.08 2.17
66 67 5.450412 CCCGTGCACTGCTATGAAATAATTT 60.450 40.000 16.19 0.00 0.00 1.82
67 68 4.036734 CCCGTGCACTGCTATGAAATAATT 59.963 41.667 16.19 0.00 0.00 1.40
68 69 3.565482 CCCGTGCACTGCTATGAAATAAT 59.435 43.478 16.19 0.00 0.00 1.28
69 70 2.942376 CCCGTGCACTGCTATGAAATAA 59.058 45.455 16.19 0.00 0.00 1.40
70 71 2.169561 TCCCGTGCACTGCTATGAAATA 59.830 45.455 16.19 0.00 0.00 1.40
71 72 1.065491 TCCCGTGCACTGCTATGAAAT 60.065 47.619 16.19 0.00 0.00 2.17
72 73 0.323302 TCCCGTGCACTGCTATGAAA 59.677 50.000 16.19 0.00 0.00 2.69
73 74 0.108186 CTCCCGTGCACTGCTATGAA 60.108 55.000 16.19 0.00 0.00 2.57
74 75 0.970427 TCTCCCGTGCACTGCTATGA 60.970 55.000 16.19 2.85 0.00 2.15
75 76 0.105593 ATCTCCCGTGCACTGCTATG 59.894 55.000 16.19 0.00 0.00 2.23
76 77 0.833287 AATCTCCCGTGCACTGCTAT 59.167 50.000 16.19 0.00 0.00 2.97
77 78 0.175760 GAATCTCCCGTGCACTGCTA 59.824 55.000 16.19 0.00 0.00 3.49
78 79 1.078848 GAATCTCCCGTGCACTGCT 60.079 57.895 16.19 0.00 0.00 4.24
79 80 2.109126 GGAATCTCCCGTGCACTGC 61.109 63.158 16.19 0.00 0.00 4.40
80 81 0.742281 CTGGAATCTCCCGTGCACTG 60.742 60.000 16.19 8.49 35.03 3.66
81 82 1.599047 CTGGAATCTCCCGTGCACT 59.401 57.895 16.19 0.00 35.03 4.40
82 83 2.109126 GCTGGAATCTCCCGTGCAC 61.109 63.158 6.82 6.82 35.03 4.57
83 84 2.268920 GCTGGAATCTCCCGTGCA 59.731 61.111 0.00 0.00 35.03 4.57
84 85 2.514824 GGCTGGAATCTCCCGTGC 60.515 66.667 0.00 0.00 35.03 5.34
85 86 2.190578 GGGCTGGAATCTCCCGTG 59.809 66.667 0.00 0.00 35.03 4.94
86 87 2.285368 TGGGCTGGAATCTCCCGT 60.285 61.111 0.00 0.00 42.98 5.28
87 88 2.507944 CTGGGCTGGAATCTCCCG 59.492 66.667 0.00 0.00 42.98 5.14
88 89 2.194326 GCTGGGCTGGAATCTCCC 59.806 66.667 0.00 0.00 40.47 4.30
89 90 1.148048 GAGCTGGGCTGGAATCTCC 59.852 63.158 0.00 0.00 39.88 3.71
90 91 1.227497 CGAGCTGGGCTGGAATCTC 60.227 63.158 0.00 0.00 39.88 2.75
91 92 2.739996 CCGAGCTGGGCTGGAATCT 61.740 63.158 0.21 0.00 39.88 2.40
92 93 2.203126 CCGAGCTGGGCTGGAATC 60.203 66.667 0.21 0.00 39.88 2.52
111 112 4.748144 GTCCTTGGGCTGGGCTGG 62.748 72.222 0.00 0.00 0.00 4.85
112 113 3.970410 TGTCCTTGGGCTGGGCTG 61.970 66.667 0.00 0.00 0.00 4.85
113 114 3.971702 GTGTCCTTGGGCTGGGCT 61.972 66.667 0.00 0.00 0.00 5.19
114 115 2.210144 TATGTGTCCTTGGGCTGGGC 62.210 60.000 0.00 0.00 0.00 5.36
115 116 0.552848 ATATGTGTCCTTGGGCTGGG 59.447 55.000 0.00 0.00 0.00 4.45
116 117 2.301346 GAATATGTGTCCTTGGGCTGG 58.699 52.381 0.00 0.00 0.00 4.85
117 118 3.003394 TGAATATGTGTCCTTGGGCTG 57.997 47.619 0.00 0.00 0.00 4.85
118 119 3.959495 ATGAATATGTGTCCTTGGGCT 57.041 42.857 0.00 0.00 0.00 5.19
119 120 3.003689 CGAATGAATATGTGTCCTTGGGC 59.996 47.826 0.00 0.00 0.00 5.36
120 121 4.199310 ACGAATGAATATGTGTCCTTGGG 58.801 43.478 0.00 0.00 0.00 4.12
121 122 4.875536 TGACGAATGAATATGTGTCCTTGG 59.124 41.667 0.00 0.00 0.00 3.61
122 123 5.582269 AGTGACGAATGAATATGTGTCCTTG 59.418 40.000 0.00 0.00 0.00 3.61
123 124 5.734720 AGTGACGAATGAATATGTGTCCTT 58.265 37.500 0.00 0.00 0.00 3.36
124 125 5.344743 AGTGACGAATGAATATGTGTCCT 57.655 39.130 0.00 0.00 0.00 3.85
125 126 6.978659 TCTTAGTGACGAATGAATATGTGTCC 59.021 38.462 0.00 0.00 0.00 4.02
126 127 7.987268 TCTTAGTGACGAATGAATATGTGTC 57.013 36.000 0.00 0.00 0.00 3.67
127 128 8.771920 TTTCTTAGTGACGAATGAATATGTGT 57.228 30.769 0.00 0.00 0.00 3.72
130 131 9.708222 CCTTTTTCTTAGTGACGAATGAATATG 57.292 33.333 0.00 0.00 0.00 1.78
131 132 8.893727 CCCTTTTTCTTAGTGACGAATGAATAT 58.106 33.333 0.00 0.00 0.00 1.28
132 133 7.335924 CCCCTTTTTCTTAGTGACGAATGAATA 59.664 37.037 0.00 0.00 0.00 1.75
133 134 6.151144 CCCCTTTTTCTTAGTGACGAATGAAT 59.849 38.462 0.00 0.00 0.00 2.57
134 135 5.472137 CCCCTTTTTCTTAGTGACGAATGAA 59.528 40.000 0.00 0.00 0.00 2.57
135 136 5.001232 CCCCTTTTTCTTAGTGACGAATGA 58.999 41.667 0.00 0.00 0.00 2.57
136 137 5.001232 TCCCCTTTTTCTTAGTGACGAATG 58.999 41.667 0.00 0.00 0.00 2.67
137 138 5.221864 ACTCCCCTTTTTCTTAGTGACGAAT 60.222 40.000 0.00 0.00 0.00 3.34
138 139 4.102054 ACTCCCCTTTTTCTTAGTGACGAA 59.898 41.667 0.00 0.00 0.00 3.85
139 140 3.644738 ACTCCCCTTTTTCTTAGTGACGA 59.355 43.478 0.00 0.00 0.00 4.20
140 141 4.004196 ACTCCCCTTTTTCTTAGTGACG 57.996 45.455 0.00 0.00 0.00 4.35
141 142 5.861727 TGTACTCCCCTTTTTCTTAGTGAC 58.138 41.667 0.00 0.00 0.00 3.67
142 143 6.503560 TTGTACTCCCCTTTTTCTTAGTGA 57.496 37.500 0.00 0.00 0.00 3.41
143 144 7.761038 ATTTGTACTCCCCTTTTTCTTAGTG 57.239 36.000 0.00 0.00 0.00 2.74
144 145 7.174426 CGAATTTGTACTCCCCTTTTTCTTAGT 59.826 37.037 0.00 0.00 0.00 2.24
145 146 7.361799 CCGAATTTGTACTCCCCTTTTTCTTAG 60.362 40.741 0.00 0.00 0.00 2.18
146 147 6.431852 CCGAATTTGTACTCCCCTTTTTCTTA 59.568 38.462 0.00 0.00 0.00 2.10
147 148 5.243060 CCGAATTTGTACTCCCCTTTTTCTT 59.757 40.000 0.00 0.00 0.00 2.52
148 149 4.765339 CCGAATTTGTACTCCCCTTTTTCT 59.235 41.667 0.00 0.00 0.00 2.52
149 150 4.521639 ACCGAATTTGTACTCCCCTTTTTC 59.478 41.667 0.00 0.00 0.00 2.29
150 151 4.476297 ACCGAATTTGTACTCCCCTTTTT 58.524 39.130 0.00 0.00 0.00 1.94
151 152 4.077108 GACCGAATTTGTACTCCCCTTTT 58.923 43.478 0.00 0.00 0.00 2.27
152 153 3.682696 GACCGAATTTGTACTCCCCTTT 58.317 45.455 0.00 0.00 0.00 3.11
153 154 2.354403 CGACCGAATTTGTACTCCCCTT 60.354 50.000 0.00 0.00 0.00 3.95
154 155 1.206371 CGACCGAATTTGTACTCCCCT 59.794 52.381 0.00 0.00 0.00 4.79
155 156 1.066645 ACGACCGAATTTGTACTCCCC 60.067 52.381 0.00 0.00 0.00 4.81
156 157 2.375173 ACGACCGAATTTGTACTCCC 57.625 50.000 0.00 0.00 0.00 4.30
157 158 3.582780 AGAACGACCGAATTTGTACTCC 58.417 45.455 0.00 0.00 0.00 3.85
158 159 4.682860 TGAAGAACGACCGAATTTGTACTC 59.317 41.667 0.00 0.00 0.00 2.59
159 160 4.624015 TGAAGAACGACCGAATTTGTACT 58.376 39.130 0.00 0.00 0.00 2.73
160 161 4.977741 TGAAGAACGACCGAATTTGTAC 57.022 40.909 0.00 0.00 0.00 2.90
161 162 6.425721 AGAAATGAAGAACGACCGAATTTGTA 59.574 34.615 0.00 0.00 0.00 2.41
162 163 5.238650 AGAAATGAAGAACGACCGAATTTGT 59.761 36.000 0.00 0.00 0.00 2.83
163 164 5.565259 CAGAAATGAAGAACGACCGAATTTG 59.435 40.000 0.00 0.00 0.00 2.32
164 165 5.468746 TCAGAAATGAAGAACGACCGAATTT 59.531 36.000 0.00 0.00 0.00 1.82
165 166 4.994852 TCAGAAATGAAGAACGACCGAATT 59.005 37.500 0.00 0.00 0.00 2.17
166 167 4.566004 TCAGAAATGAAGAACGACCGAAT 58.434 39.130 0.00 0.00 0.00 3.34
167 168 3.985008 TCAGAAATGAAGAACGACCGAA 58.015 40.909 0.00 0.00 0.00 4.30
168 169 3.653539 TCAGAAATGAAGAACGACCGA 57.346 42.857 0.00 0.00 0.00 4.69
169 170 3.423645 GCTTCAGAAATGAAGAACGACCG 60.424 47.826 19.41 0.00 45.93 4.79
170 171 3.120165 GGCTTCAGAAATGAAGAACGACC 60.120 47.826 19.41 8.49 45.93 4.79
171 172 3.498397 TGGCTTCAGAAATGAAGAACGAC 59.502 43.478 19.41 3.76 45.93 4.34
172 173 3.498397 GTGGCTTCAGAAATGAAGAACGA 59.502 43.478 19.41 0.47 45.93 3.85
173 174 3.365364 GGTGGCTTCAGAAATGAAGAACG 60.365 47.826 19.41 0.00 45.93 3.95
174 175 3.365364 CGGTGGCTTCAGAAATGAAGAAC 60.365 47.826 19.41 15.38 45.93 3.01
175 176 2.813754 CGGTGGCTTCAGAAATGAAGAA 59.186 45.455 19.41 6.07 45.93 2.52
176 177 2.426522 CGGTGGCTTCAGAAATGAAGA 58.573 47.619 19.41 0.00 45.93 2.87
177 178 1.135575 GCGGTGGCTTCAGAAATGAAG 60.136 52.381 12.54 12.54 45.84 3.02
178 179 0.881118 GCGGTGGCTTCAGAAATGAA 59.119 50.000 0.00 0.00 35.83 2.57
179 180 2.555123 GCGGTGGCTTCAGAAATGA 58.445 52.632 0.00 0.00 35.83 2.57
195 196 4.107051 CAAAAGGAGGCGGCAGCG 62.107 66.667 13.08 0.00 46.35 5.18
196 197 4.426112 GCAAAAGGAGGCGGCAGC 62.426 66.667 13.08 0.00 44.18 5.25
197 198 3.752339 GGCAAAAGGAGGCGGCAG 61.752 66.667 13.08 0.00 0.00 4.85
198 199 3.808218 AAGGCAAAAGGAGGCGGCA 62.808 57.895 13.08 0.00 36.55 5.69
199 200 2.991540 AAGGCAAAAGGAGGCGGC 60.992 61.111 0.00 0.00 36.55 6.53
200 201 2.639327 CCAAGGCAAAAGGAGGCGG 61.639 63.158 0.00 0.00 36.55 6.13
201 202 2.964978 CCAAGGCAAAAGGAGGCG 59.035 61.111 0.00 0.00 36.55 5.52
202 203 2.659016 GCCAAGGCAAAAGGAGGC 59.341 61.111 6.14 0.00 41.49 4.70
203 204 2.285773 GGGCCAAGGCAAAAGGAGG 61.286 63.158 13.87 0.00 44.11 4.30
204 205 2.639327 CGGGCCAAGGCAAAAGGAG 61.639 63.158 13.87 0.00 44.11 3.69
205 206 2.600173 CGGGCCAAGGCAAAAGGA 60.600 61.111 13.87 0.00 44.11 3.36
206 207 4.377708 GCGGGCCAAGGCAAAAGG 62.378 66.667 13.87 0.00 44.11 3.11
207 208 4.377708 GGCGGGCCAAGGCAAAAG 62.378 66.667 13.87 1.97 44.11 2.27
339 356 1.279846 TGAAGTGTACCGGGGGAAATC 59.720 52.381 6.32 0.00 0.00 2.17
340 357 1.280998 CTGAAGTGTACCGGGGGAAAT 59.719 52.381 6.32 0.00 0.00 2.17
341 358 0.688487 CTGAAGTGTACCGGGGGAAA 59.312 55.000 6.32 0.00 0.00 3.13
342 359 1.833787 GCTGAAGTGTACCGGGGGAA 61.834 60.000 6.32 0.00 0.00 3.97
344 361 2.267961 GCTGAAGTGTACCGGGGG 59.732 66.667 6.32 0.00 0.00 5.40
345 362 1.079127 CAGCTGAAGTGTACCGGGG 60.079 63.158 8.42 0.00 0.00 5.73
346 363 0.320374 TTCAGCTGAAGTGTACCGGG 59.680 55.000 25.16 0.00 0.00 5.73
347 364 2.163818 TTTCAGCTGAAGTGTACCGG 57.836 50.000 27.02 0.00 35.21 5.28
348 365 2.223377 GGTTTTCAGCTGAAGTGTACCG 59.777 50.000 27.02 0.00 35.21 4.02
349 366 3.003378 GTGGTTTTCAGCTGAAGTGTACC 59.997 47.826 27.02 27.45 35.21 3.34
350 367 3.003378 GGTGGTTTTCAGCTGAAGTGTAC 59.997 47.826 27.02 22.42 40.48 2.90
351 368 3.211045 GGTGGTTTTCAGCTGAAGTGTA 58.789 45.455 27.02 11.66 40.48 2.90
352 369 2.024414 GGTGGTTTTCAGCTGAAGTGT 58.976 47.619 27.02 0.00 40.48 3.55
360 377 3.442273 TCGAAATATGGGTGGTTTTCAGC 59.558 43.478 0.00 0.00 42.74 4.26
373 390 7.114529 GTCTTACGGTTACTGGATCGAAATATG 59.885 40.741 0.00 0.00 0.00 1.78
375 392 6.498304 GTCTTACGGTTACTGGATCGAAATA 58.502 40.000 0.00 0.00 0.00 1.40
376 393 5.346522 GTCTTACGGTTACTGGATCGAAAT 58.653 41.667 0.00 0.00 0.00 2.17
408 425 3.537874 CGGAACCCTAGGGAGGCG 61.538 72.222 35.38 7.71 42.21 5.52
427 444 0.038709 GCGATCCAGGGATCTTCGAG 60.039 60.000 22.36 10.27 46.36 4.04
1116 1176 7.067496 ACCCGACTTTGATGAGAATACATAT 57.933 36.000 0.00 0.00 0.00 1.78
1161 1221 0.766131 TAGCACCCCCTTGTCGAAAA 59.234 50.000 0.00 0.00 0.00 2.29
1164 1224 1.534476 TGTAGCACCCCCTTGTCGA 60.534 57.895 0.00 0.00 0.00 4.20
1199 1259 0.958382 TCGCTTGTAACCCATGTGCC 60.958 55.000 0.00 0.00 0.00 5.01
1203 1263 2.036958 TGGATCGCTTGTAACCCATG 57.963 50.000 0.00 0.00 0.00 3.66
1204 1264 2.799126 TTGGATCGCTTGTAACCCAT 57.201 45.000 0.00 0.00 0.00 4.00
1256 1322 9.461312 ACCTCATAATTAAATAAACACTGCAGA 57.539 29.630 23.35 0.00 0.00 4.26
1319 1396 3.826157 TGTCTAAGAACAAAATGGCAGGG 59.174 43.478 0.00 0.00 0.00 4.45
1525 1614 7.147863 CCACATGATTCATTAAGGATCCAAACA 60.148 37.037 15.82 3.60 0.00 2.83
1560 1649 2.161855 TGTCATGCTTCAACATCCACC 58.838 47.619 0.00 0.00 0.00 4.61
1905 2027 6.092807 GTGAAACCCAAGTATCTCAATGTCTC 59.907 42.308 0.00 0.00 0.00 3.36
2345 2489 1.532038 AGGGACGGAGGGAGTACTAT 58.468 55.000 0.00 0.00 0.00 2.12
2370 2514 1.899814 TGTCCCAGAATAAGTGTCGCT 59.100 47.619 0.00 0.00 0.00 4.93
2413 2557 1.302511 GCGCCTCCCTCTTGTTCAA 60.303 57.895 0.00 0.00 0.00 2.69
2447 2591 7.388776 TGTGATCCTCTCTGTAATCTGTTTTTG 59.611 37.037 0.00 0.00 0.00 2.44
2449 2593 7.009179 TGTGATCCTCTCTGTAATCTGTTTT 57.991 36.000 0.00 0.00 0.00 2.43
2552 2696 4.816990 GCTAACAGGGAGCTCGAC 57.183 61.111 7.83 3.05 36.96 4.20
2586 2730 4.523943 CCTGTCCAGACAATTTCATCCAAA 59.476 41.667 1.58 0.00 41.33 3.28
2589 2733 2.424956 GCCTGTCCAGACAATTTCATCC 59.575 50.000 1.58 0.00 41.33 3.51
2590 2734 3.084039 TGCCTGTCCAGACAATTTCATC 58.916 45.455 1.58 0.00 41.33 2.92
2591 2735 3.159213 TGCCTGTCCAGACAATTTCAT 57.841 42.857 1.58 0.00 41.33 2.57
2593 2737 3.319122 ACTTTGCCTGTCCAGACAATTTC 59.681 43.478 1.58 0.00 41.33 2.17
2594 2738 3.299503 ACTTTGCCTGTCCAGACAATTT 58.700 40.909 1.58 0.00 41.33 1.82
2650 2794 5.570034 CGAACTTTGTATCCCTAAACTCCCA 60.570 44.000 0.00 0.00 0.00 4.37
2718 2862 3.041211 TCCATGTAGCTACTGGCATCTT 58.959 45.455 25.58 3.63 44.79 2.40
2719 2863 2.682594 TCCATGTAGCTACTGGCATCT 58.317 47.619 25.58 4.57 44.79 2.90
2750 2894 4.021102 ACAGAGGACGGAAATTTGACAT 57.979 40.909 0.00 0.00 0.00 3.06
2843 2987 3.137446 AGTGCAGCTGAGATCTTGTTT 57.863 42.857 20.43 0.00 0.00 2.83
2928 3072 5.646577 TGCTTCTTCTTGACTACCTAGAC 57.353 43.478 0.00 0.00 0.00 2.59
3015 3159 7.989170 TGTGCATATTCATTGTGAAGTAGATCT 59.011 33.333 0.00 0.00 40.05 2.75
3109 3253 8.097078 CTCAGATTTATCAATGGGATGACTTC 57.903 38.462 0.00 0.00 36.72 3.01


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.